Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019249.1 Corchorus olitorius cultivar O-4 contig19282, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 14429
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.34
Found at i:9235 original size:28 final size:28
Alignment explanation
Indices: 9203--9774 Score: 388
Period size: 28 Copynumber: 20.4 Consensus size: 28
9193 TTGTCTTCGA
*
9203 GAGCGTACTACCTCTTCGCGATCTTTGG
1 GAGCGTACTACCACTTCGCGATCTTTGG
* * *
9231 GAGCGTACTACCGCTTCGCGCTCTCTGG
1 GAGCGTACTACCACTTCGCGATCTTTGG
* * * *
9259 GAGCGTACTACCTCTTTGCGATCCTTGA
1 GAGCGTACTACCACTTCGCGATCTTTGG
* * * *
9287 GAGCGTACTACCACCTCGAGAGCTTGGAGG
1 GAGCGTACTACCACTTCGCGATCTT--TGG
* * * * *
9317 GGGCGTTCTATCAATTCGCGAGCTTTGG
1 GAGCGTACTACCACTTCGCGATCTTTGG
* *
9345 GAGCGTACTACCGCTTCGCGCTCTTTGG
1 GAGCGTACTACCACTTCGCGATCTTTGG
*** * *
9373 GAGCGTACTACGCA-TTTTTG-TCTTCGA
1 GAGCGTACTAC-CACTTCGCGATCTTTGG
*
9400 GAGCGTACTACCTCTTCGCGATCTTTGG
1 GAGCGTACTACCACTTCGCGATCTTTGG
* *
9428 GAGCGTACTACCGCTTCGCTG-TCGTTGG
1 GAGCGTACTACCACTTCGC-GATCTTTGG
* * * *
9456 GAGCGTACTACCTCTTTGCGATCCTTGA
1 GAGCGTACTACCACTTCGCGATCTTTGG
* * * *
9484 GAGCGTACTACCACCTCGAGAGCTTGGAGG
1 GAGCGTACTACCACTTCGCGATCTT--TGG
* * * *
9514 GGGCGTTCTACCAATTCGCGAGCTTTGG
1 GAGCGTACTACCACTTCGCGATCTTTGG
* *
9542 GAGCGTACTATCACTTCGCGCTCTTTGG
1 GAGCGTACTACCACTTCGCGATCTTTGG
* * *
9570 GAGCGTACTACCACCTCGAGAGC-TTGG
1 GAGCGTACTACCACTTCGCGATCTTTGG
* * *
9597 AGGGCGTACTACCAATTCGCGAGC-TT-G
1 -GAGCGTACTACCACTTCGCGATCTTTGG
* *
9624 GAGGCGTACTACCACTTCGAGAGC-TTGG
1 GA-GCGTACTACCACTTCGCGATCTTTGG
* * * * *
9652 AGGGTGTACTACCATTTCGCGAACTTTGA
1 -GAGCGTACTACCACTTCGCGATCTTTGG
* * * *
9681 G-GCGTACTGCCACTTTGCGATCCTTGA
1 GAGCGTACTACCACTTCGCGATCTTTGG
* *
9708 GAGCGTACTACCACCTCGAGATC-TTGG
1 GAGCGTACTACCACTTCGCGATCTTTGG
* * * * * *
9735 AGGGAGTACTACCATTTCGTGAACTTTTG
1 -GAGCGTACTACCACTTCGCGATCTTTGG
*
9764 GAGCGTTCTAC
1 GAGCGTACTAC
9775 GTCTTAGGAT
Statistics
Matches: 419, Mismatches: 108, Indels: 34
0.75 0.19 0.06
Matches are distributed among these distances:
26 2 0.00
27 70 0.17
28 297 0.71
29 9 0.02
30 41 0.10
ACGTcount: A:0.18, C:0.27, G:0.28, T:0.28
Consensus pattern (28 bp):
GAGCGTACTACCACTTCGCGATCTTTGG
Found at i:9518 original size:197 final size:197
Alignment explanation
Indices: 9177--9580 Score: 740
Period size: 197 Copynumber: 2.1 Consensus size: 197
9167 GGGGTCTCCA
*
9177 AGCGTTCTACGCATTTTTGTCTTCGAGAGCGTACTACCTCTTCGCGATCTTTGGGAGCGTACTAC
1 AGCGTACTACGCATTTTTGTCTTCGAGAGCGTACTACCTCTTCGCGATCTTTGGGAGCGTACTAC
9242 CGCTTCGCGCTCTCTGGGAGCGTACTACCTCTTTGCGATCCTTGAGAGCGTACTACCACCTCGAG
66 CGCTTCGCGCTCTCTGGGAGCGTACTACCTCTTTGCGATCCTTGAGAGCGTACTACCACCTCGAG
* *
9307 AGCTTGGAGGGGGCGTTCTATCAATTCGCGAGCTTTGGGAGCGTACTACCGCTTCGCGCTCTTTG
131 AGCTTGGAGGGGGCGTTCTACCAATTCGCGAGCTTTGGGAGCGTACTACCACTTCGCGCTCTTTG
9372 GG
196 GG
9374 AGCGTACTACGCATTTTTGTCTTCGAGAGCGTACTACCTCTTCGCGATCTTTGGGAGCGTACTAC
1 AGCGTACTACGCATTTTTGTCTTCGAGAGCGTACTACCTCTTCGCGATCTTTGGGAGCGTACTAC
9439 CGCTTCGCTG-TCGT-TGGGAGCGTACTACCTCTTTGCGATCCTTGAGAGCGTACTACCACCTCG
66 CGCTTCGC-GCTC-TCTGGGAGCGTACTACCTCTTTGCGATCCTTGAGAGCGTACTACCACCTCG
*
9502 AGAGCTTGGAGGGGGCGTTCTACCAATTCGCGAGCTTTGGGAGCGTACTATCACTTCGCGCTCTT
129 AGAGCTTGGAGGGGGCGTTCTACCAATTCGCGAGCTTTGGGAGCGTACTACCACTTCGCGCTCTT
9567 TGGG
194 TGGG
9571 AGCGTACTAC
1 AGCGTACTAC
9581 CACCTCGAGA
Statistics
Matches: 201, Mismatches: 4, Indels: 4
0.96 0.02 0.02
Matches are distributed among these distances:
197 199 0.99
198 2 0.01
ACGTcount: A:0.16, C:0.27, G:0.27, T:0.29
Consensus pattern (197 bp):
AGCGTACTACGCATTTTTGTCTTCGAGAGCGTACTACCTCTTCGCGATCTTTGGGAGCGTACTAC
CGCTTCGCGCTCTCTGGGAGCGTACTACCTCTTTGCGATCCTTGAGAGCGTACTACCACCTCGAG
AGCTTGGAGGGGGCGTTCTACCAATTCGCGAGCTTTGGGAGCGTACTACCACTTCGCGCTCTTTG
GG
Found at i:9542 original size:86 final size:83
Alignment explanation
Indices: 9452--9748 Score: 278
Period size: 83 Copynumber: 3.5 Consensus size: 83
9442 TTCGCTGTCG
* *
9452 TTGGGAGCGTACTACCTCTTTGCGATCCTTGAGAGCGTACTACCACCTCGAGAGCTTGGAGGGGG
1 TTGGGAGCGTACTACCACTTCGCGATCCTTGAGAGCGTACTACCACCTCGAGAGCTTGGA--GGG
*
9517 CGTTCTACCAATTCGCGAGC
64 CGTACTACCAATTCGCGAGC
* * * *
9537 TTTGGGAGCGTACTATCACTTCGCGCTCTTTGGGAGCGTACTACCACCTCGAGAGCTTGGAGGGC
1 -TTGGGAGCGTACTACCACTTCGCGATCCTTGAGAGCGTACTACCACCTCGAGAGCTTGGAGGGC
9602 GTACTACCAATTCGCGAGC
65 GTACTACCAATTCGCGAGC
* * * * ** * * *
9621 TT-GGAGGCGTACTACCACTTCGAGA-GCTTGGAGGGTGTACTACCATTTCGCGAACTTTGA-GG
1 TTGGGA-GCGTACTACCACTTCGCGATCCTT-GAGAGCGTACTACCACCTCGAGAGCTTGGAGGG
* * * *
9683 CGTACTGCCACTTTGCGATCC
64 CGTACTACCAATTCGCGA-GC
* * * * *
9704 TTGAGAGCGTACTACCACCTCGAGAT-CTTGGAGGGAGTACTACCA
1 TTGGGAGCGTACTACCACTTCGCGATCCTT-GAGAGCGTACTACCA
9749 TTTCGTGAAC
Statistics
Matches: 179, Mismatches: 27, Indels: 13
0.82 0.12 0.06
Matches are distributed among these distances:
82 22 0.12
83 79 0.44
84 24 0.13
86 54 0.30
ACGTcount: A:0.20, C:0.26, G:0.28, T:0.25
Consensus pattern (83 bp):
TTGGGAGCGTACTACCACTTCGCGATCCTTGAGAGCGTACTACCACCTCGAGAGCTTGGAGGGCG
TACTACCAATTCGCGAGC
Found at i:9633 original size:197 final size:197
Alignment explanation
Indices: 9197--9642 Score: 686
Period size: 197 Copynumber: 2.3 Consensus size: 197
9187 GCATTTTTGT
9197 CTTCGAGAGCGTACTACCTCTTCGCGATCTTTGGGAGCGTACTACCGCTTCGCGCTCTCTGGGAG
1 CTTCGAGAGCGTACTACCTCTTCGCGATCTTTGGGAGCGTACTACCGCTTCGCGCTCTCTGGGAG
9262 CGTACTACCTCTTTGCGATCCTTGAGAGCGTACTACCACCTCGAGAGCTTGGAGGGGGCGTTCTA
66 CGTACTACCTCTTTGCGATCCTTGAGAGCGTACTACCACCTCGAGAGCTTGGAGGGGGCGTTCTA
* * * ***
9327 TCAATTCGCGAGCTTTGGGAGCGTACTACCGCTTCGCGCTCTTTGGGAGCGTACTACGCATTTTT
131 CCAATTCGCGAGCTTTGGGAGCGTACTACCACTTCGCGCTCTTTGGGAGCGTACTACGCACTCGA
*
9392 GT
196 GG
9394 CTTCGAGAGCGTACTACCTCTTCGCGATCTTTGGGAGCGTACTACCGCTTCGCTG-TCGT-TGGG
1 CTTCGAGAGCGTACTACCTCTTCGCGATCTTTGGGAGCGTACTACCGCTTCGC-GCTC-TCTGGG
9457 AGCGTACTACCTCTTTGCGATCCTTGAGAGCGTACTACCACCTCGAGAGCTTGGAGGGGGCGTTC
64 AGCGTACTACCTCTTTGCGATCCTTGAGAGCGTACTACCACCTCGAGAGCTTGGAGGGGGCGTTC
*
9522 TACCAATTCGCGAGCTTTGGGAGCGTACTATCACTTCGCGCTCTTTGGGAGCGTACTAC-CACCT
129 TACCAATTCGCGAGCTTTGGGAGCGTACTACCACTTCGCGCTCTTTGGGAGCGTACTACGCA-CT
9586 CGAGAG
193 CGAG-G
* * ** * *
9592 CTTGGAGGGCGTACTACCAATTCGCGAGC-TT-GGAGGCGTACTACCACTTCG
1 CTTCGAGAGCGTACTACCTCTTCGCGATCTTTGGGA-GCGTACTACCGCTTCG
9643 AGAGCTTGGA
Statistics
Matches: 230, Mismatches: 14, Indels: 10
0.91 0.06 0.04
Matches are distributed among these distances:
196 5 0.02
197 199 0.87
198 26 0.11
ACGTcount: A:0.17, C:0.28, G:0.28, T:0.27
Consensus pattern (197 bp):
CTTCGAGAGCGTACTACCTCTTCGCGATCTTTGGGAGCGTACTACCGCTTCGCGCTCTCTGGGAG
CGTACTACCTCTTTGCGATCCTTGAGAGCGTACTACCACCTCGAGAGCTTGGAGGGGGCGTTCTA
CCAATTCGCGAGCTTTGGGAGCGTACTACCACTTCGCGCTCTTTGGGAGCGTACTACGCACTCGA
GG
Found at i:9791 original size:83 final size:83
Alignment explanation
Indices: 9599--9791 Score: 214
Period size: 83 Copynumber: 2.3 Consensus size: 83
9589 GAGCTTGGAG
* * * * *
9599 GGCGTACTACCAATTCGCGAGC-TTG-GAGGCGTACTACCACTTCGAGAGCTTGGAGGGTGTACT
1 GGCGTACTACCACTTAGCGATCATTGAGA-GCGTACTACCACCTCGAGAGCTTGGAGGGAGTACT
9662 ACCATTTCGCGAACTTTGA
65 ACCATTTCGCGAACTTTGA
* * * *
9681 GGCGTACTGCCACTTTGCGATCCTTGAGAGCGTACTACCACCTCGAGATCTTGGAGGGAGTACTA
1 GGCGTACTACCACTTAGCGATCATTGAGAGCGTACTACCACCTCGAGAGCTTGGAGGGAGTACTA
*
9746 CCATTTCGTGAACTTTTG-
66 CCATTTCGCGAAC-TTTGA
* **
9764 GAGCGTTCTACGTCTTAG-GATCATTGAG
1 G-GCGTACTACCACTTAGCGATCATTGAG
9792 CGTTCTACAC
Statistics
Matches: 93, Mismatches: 14, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
82 18 0.19
83 58 0.62
84 17 0.18
ACGTcount: A:0.21, C:0.24, G:0.27, T:0.28
Consensus pattern (83 bp):
GGCGTACTACCACTTAGCGATCATTGAGAGCGTACTACCACCTCGAGAGCTTGGAGGGAGTACTA
CCATTTCGCGAACTTTGA
Found at i:14252 original size:70 final size:70
Alignment explanation
Indices: 14136--14328 Score: 368
Period size: 70 Copynumber: 2.7 Consensus size: 70
14126 GCTCGACAGA
*
14136 GAGTCAAAATTCCAATTTTCCTGCAATTTTTCAAATATATCATCAAACTTAAACATTACAATAAG
1 GAGTCAAAATTCCAATTTTCCTAC-ATTTTTCAAATATATCATCAAACTTAAACATTACAATAAG
14201 GCTCGG
65 GCTCGG
14207 GAGTCAAAATTCCAATTTTCCTACATTTTTCAAATATATCATCAAACTTAAACATTACAATAAGG
1 GAGTCAAAATTCCAATTTTCCTACATTTTTCAAATATATCATCAAACTTAAACATTACAATAAGG
14272 CTCGG
66 CTCGG
14277 GAGTCAAAATTCCAATTTTCCTACATTTTTCAAATATATCATCAAACTTAAA
1 GAGTCAAAATTCCAATTTTCCTACATTTTTCAAATATATCATCAAACTTAAA
14329 AATAAATAAT
Statistics
Matches: 121, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
70 98 0.81
71 23 0.19
ACGTcount: A:0.39, C:0.20, G:0.08, T:0.34
Consensus pattern (70 bp):
GAGTCAAAATTCCAATTTTCCTACATTTTTCAAATATATCATCAAACTTAAACATTACAATAAGG
CTCGG
Done.